\usage{
read.dna(file, format = "interleaved", skip = 0,
nlines = 0, comment.char = "#", seq.names = NULL,
- as.character = FALSE)
+ as.character = FALSE, as.matrix = NULL)
}
\arguments{
\item{file}{a file name specified by either a variable of mode character,
names read in the file are used.}
\item{as.character}{a logical controlling whether to return the
sequences as an object of class \code{"DNAbin"} (the default).}
+ \item{as.matrix}{(used if \code{format = "fasta"}) one of the three
+ followings: (i) \code{NULL}: returns the sequences in a matrix if
+ they are of the same length, otherwise in a list; (ii) \code{TRUE}:
+ returns the sequences in a matrix, or stops with an error if they
+ are of different lengths; (iii) \code{FALSE}: always returns the
+ sequences in a list.}
}
\description{
This function reads DNA sequences in a file, and returns a matrix or a
the file unless the `seq.names' option is used. Particularities for
each format are detailed below.
+\itemize{
\item{Interleaved:}{the function starts to read the sequences when it
finds 10 contiguous characters belonging to the ambiguity code of
the IUPAC (namely A, C, G, T, U, M, R, W, S, Y, K, V, H, D, B, and
leading spaces before this character). These lines are taken as taxa
names after removing the ``>'' and the possible leading and trailing
spaces. All the data in the file before the first sequence is ignored.}
-}
+}}
\value{
a matrix or a list (if \code{format = "fasta"}) of DNA sequences
stored in binary format, or of mode character (if \code{as.character =
\code{\link{read.GenBank}}, \code{\link{write.dna}},
\code{\link{DNAbin}}, \code{\link{dist.dna}}, \code{\link{woodmouse}}
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\examples{
### a small extract from `data(woddmouse)'
cat("3 40",